BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 2 7 5 446.01 3.55 2 2 73 71 28.51 0.59 3 2 76 74 28.04 0.54 4 2 127 125 21.00 0.38 5 2 128 126 21.00 0.38 6 2 131 129 21.05 0.35 7 3 6 3 464.76 1.42 8 3 7 4 463.50 3.12 9 4 7 3 469.36 0.20 10 4 8 4 463.50 3.12 11 5 8 3 477.12 1.24 12 5 9 4 459.60 1.18 13 6 9 3 476.16 2.44 14 6 10 4 459.60 1.17 15 6 124 118 45.27 0.99 16 6 127 121 45.27 0.99 17 7 10 3 476.86 0.60 18 7 11 4 469.73 4.17 19 7 73 66 48.25 0.21 20 7 74 67 49.27 0.71 21 8 11 3 476.86 0.60 22 8 12 4 459.99 1.41 23 9 12 3 476.86 0.61 24 9 13 4 459.88 1.47 25 9 121 112 60.97 0.29 26 9 124 115 60.95 0.29 27 10 13 3 474.29 1.90 28 10 14 4 470.44 3.82 29 10 70 60 61.06 0.31 30 10 124 114 60.98 0.29 31 10 125 115 60.96 0.29 32 10 128 118 60.95 0.29 33 11 14 3 477.50 0.29 34 11 15 4 468.86 4.61 35 11 70 59 61.09 0.30 36 11 71 60 61.11 0.32 37 11 73 62 61.06 0.32 38 12 15 3 482.78 2.35 39 12 16 4 456.49 2.91 40 13 16 3 482.53 2.47 41 13 17 4 475.70 0.94 42 13 121 108 61.23 0.27 43 13 125 112 61.12 0.29 44 14 17 3 471.80 2.89 45 14 18 4 471.80 2.89 46 14 21 7 389.88 8.12 47 14 63 49 61.27 0.27 48 14 66 52 61.23 0.27 49 14 67 53 61.24 0.27 50 14 70 56 61.23 0.27 51 14 109 95 64.54 0.08 52 15 18 3 472.73 0.24 53 16 116 100 67.64 1.47 54 17 20 3 476.70 0.81 55 17 21 4 446.88 3.62 56 17 24 7 404.01 9.12 57 17 113 96 86.70 1.44 58 18 21 3 481.75 1.02 59 20 23 3 475.15 3.31 60 20 24 4 458.30 2.02 61 21 24 3 478.22 1.78 62 21 25 4 458.51 1.90 63 21 63 42 93.59 1.60 64 22 25 3 470.25 3.97 65 22 26 4 458.56 1.88 66 22 60 38 98.76 0.85 67 22 63 41 97.00 0.01 68 23 26 3 464.62 1.16 69 23 27 4 458.59 1.86 70 23 56 33 116.97 1.27 71 24 27 3 459.97 1.27 72 24 28 4 459.55 1.49 73 24 108 84 121.14 0.78 74 24 109 85 121.14 0.79 75 24 112 88 131.23 0.18 76 25 28 3 459.57 1.49 77 25 29 4 459.56 1.49 78 25 59 34 116.88 1.31 79 25 105 80 121.14 0.78 80 26 29 3 467.36 1.82 81 26 30 4 466.77 2.12 82 26 56 30 127.93 0.24 83 26 59 33 116.84 1.36 84 27 30 3 471.30 4.38 85 27 31 4 458.32 2.10 86 27 108 81 131.46 0.12 87 27 112 85 132.05 0.04 88 28 31 3 470.70 4.11 89 28 32 4 458.50 1.99 90 28 101 73 131.36 0.15 91 28 104 76 131.41 0.14 92 28 105 77 131.36 0.15 93 28 108 80 131.50 0.13 94 29 32 3 461.41 0.54 95 29 33 4 463.80 4.61 96 29 55 26 131.74 0.10 97 29 58 29 131.53 0.05 98 29 59 30 131.47 0.08 99 29 101 72 131.44 0.12 100 30 33 3 478.47 2.68 101 30 34 4 463.80 4.61 102 30 50 20 157.07 12.44 103 31 34 3 478.47 2.68 104 31 35 4 463.80 4.61 105 31 104 73 131.47 0.13 106 31 107 76 132.11 0.03 107 31 108 77 132.12 0.03 108 32 35 3 482.77 0.53 109 32 36 4 448.37 2.42 110 32 39 7 356.60 22.50 111 32 101 69 131.44 0.12 112 32 104 72 131.97 0.01 113 33 37 4 409.51 4.71 114 33 39 6 360.25 20.68 115 33 40 7 290.70 0.40 116 33 43 10 286.81 1.55 117 33 48 15 205.00 2.02 118 34 37 3 475.16 1.66 119 36 39 3 492.49 4.65 120 36 100 64 131.83 0.03 121 36 103 67 132.32 0.02 122 36 104 68 132.31 0.01 123 37 40 3 502.18 5.03 124 38 41 3 491.76 1.93 125 39 42 3 494.62 3.36 126 39 43 4 481.41 0.22 127 39 97 58 131.81 0.01 128 39 100 61 132.28 0.01 129 40 43 3 480.49 0.68 130 40 44 4 472.31 1.58 131 40 48 8 248.87 2.38 132 41 44 3 478.50 1.60 133 42 92 50 132.03 0.12 134 42 93 51 132.03 0.12 135 42 94 52 132.24 0.04 136 42 97 55 132.26 0.04 137 43 46 3 475.15 3.35 138 43 48 5 440.60 10.29 139 43 58 15 215.25 0.07 140 45 54 9 240.47 6.96 141 46 54 8 240.46 6.96 142 46 58 12 240.41 6.96 143 47 52 5 260.65 0.50 144 47 54 7 240.54 6.93 145 47 55 8 253.79 0.30 146 48 55 7 253.80 0.30 147 49 52 3 458.72 0.04 148 52 55 3 463.24 2.85 149 52 56 4 455.75 0.91 150 53 56 3 455.75 0.91 151 53 57 4 455.75 0.90 152 54 57 3 469.42 3.87 153 54 58 4 456.37 1.05 154 55 58 3 463.28 3.98 155 55 59 4 457.18 0.61 156 56 59 3 469.54 0.86 157 56 60 4 463.74 3.75 158 57 60 3 484.32 2.52 159 57 61 4 468.62 1.31 160 58 61 3 479.23 5.13 161 58 62 4 465.25 0.41 162 59 62 3 474.01 1.39 163 59 63 4 470.61 3.08 164 60 63 3 473.19 1.80 165 60 64 4 467.62 4.58 166 61 64 3 468.05 4.38 167 61 65 4 461.68 2.23 168 62 65 3 474.46 2.32 169 62 66 4 461.70 2.24 170 63 66 3 472.66 3.23 171 63 67 4 464.49 0.89 172 64 67 3 468.50 1.12 173 64 68 4 464.49 0.89 174 65 68 3 469.22 2.52 175 65 69 4 464.48 0.88 176 65 80 15 154.03 2.94 177 65 83 18 152.89 3.50 178 66 69 3 465.34 0.46 179 66 70 4 465.32 0.46 180 66 105 39 159.88 0.60 181 66 128 62 160.21 0.81 182 66 129 63 159.69 0.70 183 66 132 66 158.47 1.16 184 67 70 3 470.38 1.77 185 67 71 4 465.32 0.46 186 68 71 3 467.68 1.64 187 68 72 4 459.74 2.34 188 69 72 3 465.85 0.72 189 69 73 4 455.68 4.36 190 69 76 7 278.93 1.54 191 69 80 11 228.02 17.11 192 69 128 59 165.13 3.23 193 69 132 63 159.62 0.74 194 70 73 3 460.79 1.30 195 70 128 58 160.53 0.91 196 72 75 3 484.92 3.33 197 72 76 4 426.25 0.58 198 72 79 7 284.68 1.75 199 73 76 3 471.18 3.35 200 75 78 3 477.19 2.49 201 75 79 4 434.28 4.07 202 76 79 3 453.00 1.32 203 76 80 4 434.28 4.08 204 76 128 52 177.03 2.52 205 76 131 55 177.00 2.54 206 76 132 56 177.00 2.54 207 76 135 59 176.94 2.54 208 77 81 4 444.00 2.60 209 77 135 58 176.96 2.54 210 78 81 3 463.22 3.79 211 80 83 3 466.84 1.98 212 80 84 4 461.29 0.80 213 80 132 52 178.38 2.07 214 80 135 55 178.21 2.06 215 80 136 56 178.34 2.05 216 81 84 3 469.64 3.38 217 81 85 4 461.43 0.73 218 82 85 3 475.16 3.32 219 82 86 4 457.74 1.11 220 83 86 3 479.25 0.33 221 83 87 4 456.83 0.68 222 83 136 53 178.40 2.04 223 84 87 3 476.82 1.54 224 84 88 4 456.83 0.68 225 84 135 51 178.43 2.05 226 84 136 52 178.40 2.04 227 85 89 4 434.34 0.53 228 85 90 5 389.94 5.50 229 86 90 4 362.07 22.12 230 86 91 5 312.68 3.40 231 87 91 4 362.89 21.71 232 87 92 5 291.05 7.40 233 87 93 6 288.50 8.59 234 87 98 11 266.50 6.00 235 87 136 49 178.51 2.05 236 88 92 4 341.28 32.51 237 88 136 48 178.52 2.04 238 88 137 49 178.41 2.04 239 88 138 50 178.38 2.05 240 89 92 3 450.03 6.42 241 93 97 4 475.30 3.19 242 93 98 5 464.00 1.73 243 94 97 3 491.09 3.48 244 95 98 3 481.00 0.46 245 95 99 4 471.41 1.24 246 95 137 42 180.47 2.18 247 96 99 3 483.35 0.83 248 96 100 4 470.73 1.58 249 97 100 3 470.74 1.58 250 97 101 4 464.09 1.74 251 98 101 3 476.54 0.84 252 98 102 4 464.06 1.74 253 98 133 35 180.90 2.25 254 98 136 38 180.91 2.25 255 98 137 39 180.89 2.25 256 99 102 3 467.44 0.17 257 99 103 4 465.70 0.91 258 100 103 3 470.13 1.68 259 100 104 4 465.38 0.69 260 101 104 3 469.43 1.33 261 101 105 4 465.38 0.69 262 102 105 3 473.19 0.55 263 102 106 4 465.38 0.68 264 102 129 27 181.97 2.34 265 102 133 31 181.97 2.34 266 103 106 3 473.88 0.21 267 103 107 4 470.09 1.69 268 104 107 3 473.88 0.21 269 104 108 4 457.02 3.50 270 105 108 3 461.43 5.70 271 105 109 4 447.69 0.08 272 105 129 24 184.52 2.77 273 106 109 3 467.45 4.01 274 106 110 4 448.94 0.53 275 106 117 11 210.35 3.93 276 106 122 16 184.66 2.78 277 106 125 19 184.62 2.80 278 106 126 20 184.59 2.79 279 106 129 23 184.58 2.79 280 107 110 3 478.35 1.44 281 107 111 4 448.95 0.54 282 108 111 3 473.88 0.19 283 108 112 4 448.94 0.53 284 109 112 3 474.16 0.05 285 109 113 4 448.87 0.52 286 109 117 8 246.86 3.04 287 109 125 16 188.61 0.83 288 110 113 3 462.00 6.04 289 110 117 7 246.84 3.02 290 113 116 3 480.85 2.65 291 113 117 4 399.32 24.30 292 115 118 3 506.88 0.57 293 116 121 5 435.22 0.69 294 117 122 5 431.52 1.55 295 117 125 8 415.56 8.27 296 118 121 3 473.68 3.57 297 118 122 4 458.83 2.43 298 119 122 3 473.01 3.91 299 119 123 4 462.30 0.70 300 120 123 3 475.92 3.30 301 120 124 4 473.20 3.82 302 121 124 3 473.25 3.83 303 121 125 4 465.97 0.21 304 122 125 3 476.84 2.84 305 122 126 4 466.91 0.69 306 123 126 3 476.00 2.43 307 123 127 4 467.10 0.61 308 124 127 3 471.88 0.36 309 124 128 4 467.10 0.61 310 125 128 3 470.28 1.17 311 125 129 4 469.24 1.68 312 126 129 3 472.22 0.20 313 126 130 4 469.24 1.69 314 127 130 3 459.49 3.18 315 127 131 4 464.88 0.26 316 128 131 3 471.59 2.04 317 128 132 4 464.88 0.26 318 129 132 3 462.40 6.64 319 129 133 4 456.18 3.66 320 130 133 3 472.22 1.73 321 130 134 4 458.34 2.54 322 131 134 3 470.56 2.56 323 131 135 4 464.41 0.51 324 132 135 3 472.22 1.73 325 132 136 4 470.36 2.46 326 133 136 3 470.36 2.46 327 133 137 4 457.67 2.23 328 134 137 3 477.31 0.79 329 134 138 4 454.61 3.76 330 135 138 3 480.60 3.82